Estimating species richness and accumulation by modeling species occurrence and detectability

A statistical model is developed for estimating species richness and accumulation by formulating these community-level attributes as functions of model-based estimators of species occurrence while accounting for imperfect detection of individual species. The model requires a sampling protocol wherein repeated observations are made at a collection of sample locations selected to be representative of the community. This temporal replication provides the data needed to resolve the ambiguity between species absence and nondetection when species are unobserved at sample locations. Estimates of species richness and accumulation are computed for two communities, an avian community and a butterfly community. Our model-based estimates suggest that detection failures in many bird species were attributed to low rates of occurrence, as opposed to simply low rates of detection. We estimate that the avian community contains a substantial number of uncommon species and that species richness greatly exceeds the number of species actually observed in the sample. In fact, predictions of species accumulation suggest that even doubling the number of sample locations would not have revealed all of the species in the community. In contrast, our analysis of the butterfly community suggests that many species are relatively common and that the estimated richness of species in the community is nearly equal to the number of species actually detected in the sample. Our predictions of species accumulation suggest that the number of sample locations actually used in the butterfly survey could have been cut in half and the asymptotic richness of species still would have been attained. Our approach of developing occurrence-based summaries of communities while allowing for imperfect detection of species is broadly applicable and should prove useful in the design and analysis of surveys of biodiversity.     

Potential nitrogen constraints on soil carbon sequestration under low and elevated atmospheric CO2

The interaction between nitrogen cycling and carbon sequestration is critical in predicting the consequences of anthropogenic increases in atmospheric CO2 (hereafter, Ca). The progressive N limitation (PNL) theory predicts that carbon sequestration in plants and soils with rising Ca may be constrained by the availability of nitrogen in many ecosystems. Here we report on the interaction between C and N dynamics during a four-year field experiment in which an intact C3/C4 grassland was exposed to a gradient in Ca from 200 to 560 micromol/mol. There were strong species effects on decomposition dynamics, with C loss positively correlated and N mineralization negatively correlated with Ca for litter of the C3 forb Solanum dimidiatum, whereas decomposition of litter from the C4 grass Bothriochloa ischaemum was unresponsive to Ca. Both soil microbial biomass and soil respiration rates exhibited a nonlinear response to Ca, reaching a maximum at approximately 440 micromol/mol Ca. We found a general movement of N out of soil organic matter and into aboveground plant biomass with increased Ca. Within soils we found evidence of C loss from recalcitrant soil C fractions with narrow C:N ratios to more labile soil fractions with broader C:N ratios, potentially due to decreases in N availability. The observed reallocation of N from soil to plants over the last three years of the experiment supports the PNL theory that reductions in N availability with rising Ca could initially be overcome by a transfer of N from low C:N ratio fractions to those with higher C:N ratios. Although the transfer of N allowed plant production to increase with increasing Ca, there was no net soil C sequestration at elevated Ca, presumably because relatively stable C is being decomposed to meet microbial and plant N requirements. Ultimately, if the C gained by increased plant production is rapidly lost through decomposition, the shift in N from older soil organic matter to rapidly decomposing plant tissue may limit net C sequestration with increased plant production.     

Distribution and evolution of genetic caste determination in Pogonomyrmex seed-harvester ants

We examined the distribution and ancestral relationships of genetic caste determination (GCD) in 46 populations of the seed-harvester ants Pogonomyrmex barbatus and P. rugosus across the east-to-west range of their distributions. Using a mtDNA sequence and two nuclear markers diagnostic for GCD, we distinguished three classes of population phenotypes: those with GCD, no evidence of GCD, and mixed (both GCD and non-GCD colonies present). The GCD phenotype was geographically widespread across the range of both morphospecies, occurring in 20 of 46 sampled populations. Molecular data suggest three reproductively isolated and cryptic lineages within each morphospecies, and no present hybridization. Mapping the GCD phenotype onto a mtDNA phylogeny indicates that GCD in P. rugosus was acquired from P. barbatus, suggesting that interspecific hybridization may not be the causal agent of GCD, but may simply provide an avenue for GCD to spread from one species (or subspecies) to another. We hypothesize that the origin of GCD involved a genetic mutation with a major effect on caste determination. This mutation generates genetic conflict and results in the partitioning and maintenance of distinct allele (or gene set) combinations that confer differences in developmental caste fate. The outcome is two dependent lineages within each population; inter-lineage matings produce workers, while intra-lineage matings produce reproductives. Both lineages are needed to produce a caste-functional colony, resulting in two reproductively isolated yet interdependent lineages. Pogonomyrmex populations composed of dependent lineages provide a unique opportunity to investigate genetic variation underlying phenotypic plasticity and its impact on the evolution of social structure.     

Fate of nitrogen in riparian forest soils and trees: an 15N tracer study simulating salmon decay

We introduced an 15N-NH4+ tracer to the riparian forest of a salmon-bearing stream (Kennedy Creek, Washington, USA) to quantify the cycling and fate of a late-season pulse of salmon N and, ultimately, mechanisms regulating potential links between salmon abundance and tree growth. The 15N tracer simulated deposition of 7.25 kg of salmon (fresh) to four 50-m2 plots. We added NH4+ (the initial product of salmon carcass decay) and other important nutrients provided by carcasses (P, S, K, Mg, Ca) to soils in late October 2003, coincident with local salmon spawning. We followed the 15N tracer through soil and tree pools for one year. Biological uptake of the 15N tracer occurred quickly: 64% of the 15N tracer was bound in soil microbiota within 14 days, and roots of the dominant riparian tree, western red cedar (Thuja plicata), began to take up 15N tracer within seven days. Root uptake continued through the winter. The 15N tracer content of soil organic matter reached a maximum of approximately 52%, five weeks after the application, and a relative equilibrium of approximately 40% within five months. Six months after the addition, in spring 2004, at least 37% of the 15N tracer was found in tree tissues: approximately 23% in foliage, approximately 11% in roots, and approximately 3% in stems. Within the stems, xylem and phloem sap contained approximately 96% of the tracer N, and approximately 4% was in structural xylem N. After one year, at least 28% of the 15N tracer was still found in trees, and loss from the plots was only approximately 20%. The large portion of tracer N taken up in the fall and reallocated to leaves and stems the following spring provides mechanistic evidence for a one-year-lagged tree-growth response to salmon nutrients. Salmon nutrients have been deposited in the Kennedy Creek system each fall for centuries, but the system shows no evidence of nutrient saturation. Rates of N uptake and retention are a function of site history and disturbance and also may be the result of a legacy effect, in which annual salmon nutrient addition may lead to increased efficiency of nutrient uptake and use.     

Nutrient subsidies to belowground microbes impact aboveground food web interactions

Historically, terrestrial food web theory has been compartmentalized into interactions among aboveground or belowground communities. In this study we took a more synthetic approach to understanding food web interactions by simultaneously examining four trophic levels and investigating how nutrient (nitrogen and carbon) and detrital subsidies impact the ability of the belowground microbial community to alter the abundance of aboveground arthropods (herbivores and predators) associated with the intertidal cord grass Spartina alterniflora. We manipulated carbon, nitrogen, and detrital resources in a field experiment and measured decomposition rate, soil nitrogen pools, plant biomass and quality, herbivore density, and arthropod predator abundance. Because carbon subsidies impact plant growth only indirectly (microbial pathways), whereas nitrogen additions both directly (plant uptake) and indirectly (microbial pathways) impact plant primary productivity, we were able to assess the effect of both belowground soil microbes and nutrient availability on aboveground herbivores and their predators. Herbivore density in the field was suppressed by carbon supplements. Carbon addition altered soil microbial dynamics (net potential ammonification, litter decomposition rate, DON [dissolved organic N] concentration), which limited inorganic soil nitrogen availability and reduced plant size as well as predator abundance. Nitrogen addition enhanced herbivore density by increasing plant size and quality directly by increasing inorganic soil nitrogen pools, and indirectly by enhancing microbial nitrification. Detritus adversely affected aboveground herbivores mainly by promoting predator aggregation. To date, the effects of carbon and nitrogen subsidies on salt marshes have been examined as isolated effects on either the aboveground or the belowground community. Our results emphasize the importance of directly addressing the soil microbial community as a factor that influences aboveground food web structure by affecting plant size and aboveground plant nitrogen.     

Dietary characterization of the hominoid Khoratpithecus (Miocene of Thailand): evidence from dental topographic and microwear texture analyses

The genus Khoratpithecus, a hominoid thought to be related to the orangutan lineage, is represented by two known fossil species K. chiangmuanensis and K. piriyai. Both were discovered in Southeast Asia (Thailand) and are dated to the Middle and Late Miocene, respectively. In this study, dental topographic and microwear texture analyses were used to examine molars from both of these species, with the goal of understanding their dietary preferences. Although sample sizes are small for Khoratpithecus, available data are compared to that collected for extant apes. Environmental evidence, such as botanical remains and sedimentological data, is also considered for comparisons with dietary reconstruction. Results from dental topographic analysis suggest that the two fossil species were better adapted to a diet of fruits than to one of leaves, much like the living orangutan or chimpanzee. Results from microwear texture analysis further support this, suggesting that Khoratpithecus preferred soft fruits to hard fruits or seeds. And finally, the botanical and sedimentological evidence point to environments for Khoratpithecus that would have been compatible with a fruit-eating species. Given the small sample sizes available for analysis, however, definitive judgments are not yet possible at this time.     

The challenge of providing environmental flow rules to sustain river ecosystems.

Accounting for natural differences in flow variability among rivers, and understanding the importance of this for the protection of freshwater biodiversity and maintenance of goods and services that rivers provide, is a great challenge for water managers and scientists. Nevertheless, despite considerable progress in understanding how flow variability sustains river ecosystems, there is a growing temptation to ignore natural system complexity in favor of simplistic, static, environmental flow "rules" to resolve pressing river management issues. We argue that such approaches are misguided and will ultimately contribute to further degradation of river ecosystems. In the absence of detailed empirical information of environmental flow requirements for rivers, we propose a generic approach that incorporates essential aspects of natural flow variability shared across particular classes of rivers that can be validated with empirical biological data and other information in a calibration process. We argue that this approach can bridge the gap between simple hydrological "rules of thumb" and more comprehensive environmental flow assessments and experimental flow restoration projects.     

Challenges of climate change: an Arctic perspective

Climate change is being experienced particularly intensely in the Arctic. Arctic average temperature has risen at almost twice the rate as that of the rest of the world in the past few decades. Widespread melting of glaciers and sea ice and rising permafrost temperatures present additional evidence of strong Arctic warming. These changes in the Arctic provide an early indication of the environmental and societal significance of global consequences. The Arctic also provides important natural resources to the rest of the world (such as oil, gas, and fish) that will be affected by climate change, and the melting of Arctic glaciers is one of the factors contributing to sea level rise around the globe. An acceleration of these climatic trends is projected to occur during this century, due to ongoing increases in concentrations of greenhouse gases in the Earth's atmosphere. These Arctic changes will, in turn, impact the planet as a whole.     

The economic impact of sea-level rise on nonmarket lands in Singapore

Sea-level rise, as a result of climate change, will likely inflict considerable economic consequences on coastal regions, particularly low-lying island states like Singapore. Although the literature has addressed the vulnerability of developed coastal lands, this is the first economic study to address nonmarket lands, such as beaches, marshes and mangrove estuaries. This travel cost and contingent valuation study reveals that consumers in Singapore attach considerable value to beaches. The contingent valuation study also attached high values to marshes and mangroves but this result was not supported by the travel cost study. Although protecting nonmarket land uses from sea-level rise is expensive, the study shows that at least highly valued resources, such as Singapore's popular beaches, should be protected.